This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The MacCoss lab distributed the following software in 2010-2011: MakeMS2: A windows program for extracting mass spectrometry data from Thermo Fisher RAW instrument files. Hardklor /Kronik: A pair of programs for the analysis of high resolution mass spectrometry data. Hardklor will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions. CRAWDAD: A software suite for label-free relative quantitation of high- and low-resolution LC-MS data. Replicate runs are aligned in the retention time dimension prior to feature detection using dynamic time warping. Features of differential intensity are detected using statistical tests, and annotated using MS/MS peptide identifications. MScout: A software tool for assessing LC-MS data quality. P3 Predictor: A simple windows program to aide in establishing SRM transitions for targeted proteomics. IDCalc: A Microsoft Windows program that implements the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions. Skyline: A Windows client application for building Selected Reaction Monitoring methods and analyzing the resulting mass spectrometry data. PAnDA: PAnDA is an acronym for Post Analysis Data Acquisition. PAnDA uses the Hardklor feature finder to determine the molecular species in an LC-MS analysis and then uses this information to automatically construct new methods to acquire features missed in prior analyses. Topograph: A Microsoft Windows application for the analysis of mass spectrometry data from biological samples that have been labeled with stable isotope labeled amino acid(s) BullsEye: A program for correcting the monoisotopic m/z for MS/MS spectra from hybrid LTQ-FT and LTQ-Orbitrap mass spectrometers. PepLynx: A program for the interpretation of high resolution MS/MS spectra of cross-linked peptides. P3 Predictor: A simple windows program to aide in establishing SRM transitions for targeted proteomics.